binnify crashes for small genome ?

[nservant]

Hi all,
I tried to run the binnify command on a small genome and it crashed

cooltools genome binnify chrom.size 1000 > genome_bins.txt
Traceback (most recent call last):
  File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/bin/cooltools", line 8, in <module>
    sys.exit(cli())
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/nservant/.local/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/cooltools/cli/genome.py", line 30, in binnify
    bins = bioframe.tools.binnify(chromsizes, binsize)
  File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/bioframe/tools.py", line 80, in binnify
    axis=0, ignore_index=True)
  File "/home/nservant/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 281, in concat
    sort=sort,
  File "/home/nservant/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 329, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

The reference genome is available here ;
https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa

In total, there are 236 contigs. I though that it could be due to one contig with a size smaller than the bin size, but even with 100 bp bin, I still have the error.
Thanks
N

[nvictus]

Could you try:

cooltools genome binnify --all-names chrom.size 1000 > genome_bins.txt

[nservant]

Well done! It works.
Can I use the option --all-names by default ? for all reference genomes ?

[nvictus]

Yes, and we should change the current default behavior. With --all-names no sorting happens.

Without --all-names it looks for patterns "chr[0-9]+$", "chr[XY]$", "chrM$" and sorts in them in that order. So it was filtering out everything in your case.

[nservant]

Thanks @nvictus !